Publications

My publications consist of 1 book and 32 published articles, with 965 citations since 2012 and an h-index of 17 (via Google Scholar). These publications include 1 book as editor and 9 articles as lead, senior, and/or corresponding author. Online publication lists can be found on PubMed, Logo Google Scholar, Logo ORCID, Logo Loop, Logo Scopus, or Logo Publons. I have published 1 protocol with protocols.io and 1 newsletter article with the Australia and New Zealand Society for Immunology. My software toolkit, Spectre, has been cited in 44 publications in prestigious journals such as Cell and Nature Immunology, and is a featured analysis package for the Human Cell Atlas project.

Books

HM McGuire*, TM Ashhurst* (eds). 2019. Mass Cytometry: Methods and Protocols. Springer New York.

This book details a compilation of up-to-date and cutting-edge protocols in mass cytometry. Chapters guide readers through setting up a facility, panel design and reagent preparation, sample preparation, specific applications, and data analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Mass Cytometry: Methods and Protocols aims to ensure successful results in the further study of this vital field.

‘Mass Cytometry: Methods and Protocols’ has been downloaded over 57,000 times and cited 84 times. Protocols provided in this book have been cited in a wide variety of applications, including COVID-19 (Rodriguez et al. 2020, Koutsakos et al. 2021).

Lead or senior author

Sedigheh Jalali, Christopher M Harpur, Adam T Piers, Maria Auladell, Louis Perriman, Shuo Li, Kim An, Jeremy Anderson, Stuart P Berzins, Paul V Licciardi, Thomas M Ashhurst*, Igor E Konstantinov*, Daniel G Pellicci*. 2022. A high‐dimensional cytometry atlas of peripheral blood over the human life span. Immunology and Cell Biology, 100: 805-821.

Editors Choice, ICB

Givanna H Putri, Jonathan Chung, Davis N Edwards, Felix Marsh‐Wakefield, Irena Koprinska, Suat Dervish, Nicholas JC King, Thomas M Ashhurst, Mark N Read. 2022. TrackSOM: mapping immune response dynamics through clustering of time‐course cytometry data. Cytometry Part A.

TM Ashhurst*, F Marsh-Wakefield*, GH Putri*, AG Spiteri, D Shinko, … 2021. Integration, exploration, and analysis of high-dimensional single-cell cytometry data using Spectre. Cytometry A (accepted). Corresponding author.

Preprint available here.
Presentation at the Oz Single Cell webinar series: computational biology.
Our high-dimensional analysis workshops featured in: High Dimensional Data Analysis Strategies Homeshow 2020 - in ASI News. 2020. Australia and New Zealand Society for Immunology.
Code available from our Github page
Protocols and instructions available on the Spectre Home Page.
In the top 5% of all research outputs scored by Altmetric

P Niewold*, TM Ashhurst*, AL Smith, NJC King. 2020. Evaluating spectral cytometry for immune profiling in viral disease. Cytometry Part A.

ISAC webinar on spectral cytometry

R Salomon*, C Hall*, TM Ashhurst* (2019). Cytometry in the Era of the Human Cell Atlas (WS06). Part of: K Czechowsk et al. (2019). Cyt‐Geist: Current and future challenges in cytometry: Reports of the CYTO 2018 conference workshops. Cytometry Part A 95 (6), 598-644

Published following a workshop at CYTO 2018 on the use of cytometry in the era of the Human Cell Atlas.

TM Ashhurst, DA Cox, AL Smith, NJC King. 2019. Analysis of the murine bone marrow hematopoietic system using mass and flow cytometry. Mass Cytometry, 159-192

>2,300 downloads since 2019.
Protocols dervied from this paper are listed on the resource page

TM Ashhurst, AL Smith, NJC King. 2017. High‐Dimensional Fluorescence Cytometry. Current Protocols in Immunology 119 (1), 5.8. 1-5.8. 38. Corresponding author.

In this paper we describe panel design strategies for panels up to 26 colours.
This is the first publication we are aware of describing a panel above 18 colours, following Dr. Pratip Chattodpahyay’s presentation of 25-colour flow at CYTO 2014.
Highly optimised panels of over 18 colours published around the same include Staser et al, 2017 and Mair & Prlic, 2018

TM Ashhurst*, C van Vreden*, P Niewold*, NJC King. 2014. The plasticity of inflammatory monocyte responses to the inflamed central nervous system. Cellular immunology 291 (1-2), 49-57

TM Ashhurst, C Van Vreden, L Munoz-Erazo, P Niewold, K Watabe, … 2013. Antiviral macrophage responses in flavivirus encephalitis. The Indian journal of medical research 138 (5), 632

Co-author

Niels JM Verstegen, Ruth R Hagen, Jet van den Dijssel, Lisan H Kuijper, Christine Kreher, Thomas Ashhurst, Laura YL Kummer, … Marieke SM van Ham, Anja ten Brinke, Carolien E van de Sandt, on behalf of the T2B! immunity against SARS-CoV-2 study group. 2022. Immune dynamics in SARS-CoV-2 experienced immunosuppressed rheumatoid arthritis or multiple sclerosis patients vaccinated with mRNA-1273. eLife.

W Zhang, B Chua, K Selva, L Kedzierski, T Ashhurst, E Haycroft, … Thi Nguyen, Katherine Kedzierska. 2022. SARS-CoV-2 infection results in immune responses in the respiratory tract and peripheral blood that suggest mechanisms of disease severity. Nature Communications.

Phillip K. West, Andrew N. McCorkindale, Boris Guennewig, Thomas M. Ashhurst, Barney Viengkhou, Emina Hayashida, So Ri Jung, Oleg Butovsky, Iain L. Campbell & Markus J. Hofer (2022). The cytokines interleukin-6 and interferon-α induce distinct microglia phenotypes. Journal of Neuroinflammation. 19, 96.

Felix Marsh-Wakefield, Pierre Juillard, Thomas M Ashhurst, Annette Juillard, Diana Shinko, Givanna H Putri, Mark N Read, Helen M McGuire, Scott N Byrne, Simon Hawke, Georges E Grau (2022). Peripheral B cell dysregulation is associated with relapse after long-term quiescence in multiple sclerosis patients. Immunology and Cell Biology. Online.

LuukWieske, Koos P Jvan Dam, Maurice Steenhuis, … Filip Eftimov on behalf of the T2B! Immunity against SARS-CoV-2 study group. Humoral responses after second and third SARS-CoV-2 vaccination in patients with immune-mediated inflammatory disorders on immunosuppressants: a cohort study. The Lancet Rheumatology. In press.

T Liechti, L Weber, TM Ashhurst, N Stanley, M Prlic, S Van Gassen, F Mair. (2021). An updated guide for the perplexed: cytometry in the high-dimensional era. Nature Immunology.

Featured on the Nature’s Immunology subject page.

AG Spiteri, RL Terry, CL Wishart, TM Ashhurst, IL Campbell, MJ Hofer, NJC King. 2021. High-parameter cytometry unmasks microglial cell spatio-temporal response kinetics in severe neuroinflammatory disease. J. Neuroinflammation, 18, 166.

F Marsh-Wakefield*, A Mitchell*, S Norton, TM Ashhurst, … HM McGuire, R Kemp. 2021. Making the most of high dimensional cytometry data. Immunology and Cellular Biology.

Publication resulting from a joint venture between the Australia and New Zealand Society for Immunology and the Australasian Cytometry Society.
Included in the ICB ‘Featured Articles’.

M Koutsakos, LC Rowntree, L Hensen, BY Chua, CE van de Sandt, JR Habel, W Zhang, X Jia, L Kedzierski, TM Ashhurst, … K Kedzierska. 2021. Integrated immune dynamics define correlates of COVID-19 severity and antibody responses. Cell Reports Medicine. Lead the computational analysis of COVID-19 blood samples, and supervised the development of TrackSOM for time-series tracking.

Summary
Media: Doherty Institute News, Medical Xpress, Herald Sun, Ticker.
Metrics: PlumX

KC Ferrell, EL Stewart, C Counoupas, TM Ashhurst, WJ Britton, N Petrovsky, JA Triccas. 2021. Intrapulmonary vaccination with delta-inulin adjuvant stimulates non-polarised chemotactic signalling and diverse cellular interaction. Mucosal Immunology.

GH Putri, I Koprinska, TM Ashhurst, NJC King, MN Read. 2021. Using single-cell cytometry to illustrate integrated multi-perspective evaluation of clustering algorithms using Pareto fronts. Bioinformatics. Supervising role.

Code available from the Github repository.

F Marsh‐Wakefield, T Ashhurst, S Trend, HM McGuire, P Juillard, A Zinger, … 2020. IgG3+ B cells are associated with the development of multiple sclerosis. Clinical & Translational Immunology 9 (5), e01133

SR Jung, TM Ashhurst, PK West, B Viengkhou, NJC King, IL Campbell, … 2020. Contribution of STAT1 to innate and adaptive immunity during type I interferon-mediated lethal virus infection. PLoS Pathogens 16 (4), e1008525

GH Putri, MN Read, I Koprinska, TM Ashhurst, NJC King. 2019. Dimensionality Reduction for Clustering and Cluster Tracking of Cytometry Data. International Conference on Artificial Neural Networks, 624-640

GH Putri, MN Read, I Koprinska, D Singh, U Röhm, TM Ashhurst, NJC King. 2019. ChronoClust: Density-based clustering and cluster tracking in high-dimensional time-series data. Knowledge-Based Systems 174, 9-26

E Hayashida, ZL Ling, TM Ashhurst, B Viengkhou, SR Jung, … 2019. Zika virus encephalitis in immunocompetent mice is dominated by innate immune cells and does not require T or B cells. Journal of Neuroinflammation 16 (1), 1-15

D Shinko, TM Ashhurst, HM McGuire, KA Charles. 2019. Staining of phosphorylated signalling markers protocol for mass cytometry. Mass Cytometry, 139-146

SR Jung, T Suprunenko, TM Ashhurst, NJC King, MJ Hofer. 2018. Collateral Damage: What Effect Does Anti-CD4 and Anti-CD8α Antibody–Mediated Depletion Have on Leukocyte Populations?. The Journal of Immunology 201 (7), 2176-2186

TM Campbell, BP McSharry, M Steain, TM Ashhurst, B Slobedman, … 2018. Varicella zoster virus productively infects human natural killer cells and manipulates phenotype. PLoS pathogens 14 (4), e1006999

M Huber, T Suprunenko, T Ashhurst, F Marbach, H Raifer, S Wolff, … 2017. IRF9 Prevents CD8+ T cell exhaustion in an extrinsic manner during acute Lymphocytic choriomeningitis virus infection. Journal of Virology 91 (22)

RL Terry, C Deffrasnes, DR Getts, C Minten, C Van Vreden, TM Ashhurst, … 2015. Defective inflammatory monocyte development in IRF8-deficient mice abrogates migration to the West Nile virus-infected brain. Journal of innate immunity 7 (1), 102-112

DR Getts, RL Terry, MT Getts, C Deffrasnes, M Müller, C van Vreden, TM Ashhurst … 2014. Therapeutic inflammatory monocyte modulation using immune-modifying microparticles. Science translational medicine 6 (219), 219ra7-219ra7.

News items: ABC News, The Guardian.

DR Getts, RL Terry, MT Getts, M Müller, S Rana, C Deffrasnes, TM Ashhurst… 2012. Targeted blockade in lethal West Nile virus encephalitis indicates a crucial role for very late antigen (VLA)-4-dependent recruitment of nitric oxide-producing macrophages. Journal of Neuroinflammation 9 (1), 246.

Protocols

TM Ashhurst, DA Cox, AL Smith, NJC King 2021. Cell counting with a haemocytometer (with mouse bone marrow example). protocols.io https://dx.doi.org/10.17504/protocols.io.btqgnmtw

Newsletters

High-dimensional single cell mass cytometry (CyTOF) comes to Australia with the establishment of the Ramaciotti Facility for Human Systems Biology. 2015. T Ashhurst, N King, A Smith, BF de St Groth. ASI Newsletter.